Input data and parameters
Input
| Analysis date: | Sun Oct 29 12:56:25 GMT 2023 |
| BAM file: | SRX7354127.markdup.sorted.bam |
| Counting algorithm: | uniquely-mapped-reads |
| GTF file: | gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf |
| Number of bases for 5'-3' bias computation: | 100 |
| Number of transcripts for 5'-3' bias computation: | 1,000 |
| Paired-end sequencing: | yes |
| Protocol: | strand-specific-reverse |
| Sorting performed: | yes |
Summary
Reads alignment
| Number of mapped reads (left/right): | 76,972,746 / 76,744,382 |
| Number of aligned pairs (without duplicates): | 76,733,279 |
| Total number of alignments: | 162,285,685 |
| Number of secondary alignments: | 8,568,557 |
| Number of non-unique alignments: | 13,615,947 |
| Aligned to genes: | 122,737,359 |
| Ambiguous alignments: | 447,878 |
| No feature assigned: | 24,530,821 |
| Missing chromosome in annotation: | 953,680 |
| Not aligned: | 21,205,742 |
Reads genomic origin
| Exonic: | 122,737,359 / 83.34% |
| Intronic: | 17,092,562 / 11.61% |
| Intergenic: | 7,438,259 / 5.05% |
| Intronic/intergenic overlapping exon: | 6,544,453 / 4.44% |
Transcript coverage profile
| 5' bias: | 0.5 |
| 3' bias: | 0.27 |
| 5'-3' bias: | 1.66 |
Junction analysis
| Reads at junctions: | 51,067,445 |
| ACCT | 5.05% |
| AGGT | 4.72% |
| ATCT | 3.66% |
| TCCT | 3.46% |
| AGGA | 3.42% |
| GCCT | 3.38% |
| AGCT | 2.9% |
| CCCT | 2.78% |
| AGGC | 2.5% |
| AGAT | 2.11% |
| TTCT | 2.1% |

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